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[18.01] Update framework dependencies documentation #5390

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merged 3 commits into from Feb 1, 2018

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natefoo commented Jan 25, 2018

Also add detection for conda-forge Python and add a script for installing dependencies from Conda (4.4+ only).

Install dependencies using the `unpinned requirements file`_, and then instruct
Galaxy to start without attempting to fetch wheels:
If you would like to install unpinned versions of Galaxy's dependencies, Install dependencies using the `unpinned

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@nsoranzo

nsoranzo Jan 25, 2018

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s/Install dependencies/install dependencies/

.. _Pull Request #4891: https://github.com/galaxyproject/galaxy/pull/4891

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nsoranzo Jan 25, 2018

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This could be moved after it's used at line 361.

Using a `virtualenv`_ in ``.venv`` under the Galaxy source tree is not required. More complicated Galaxy setups may
choose to use a virtualenv external to the Galaxy source tree, which can be done either by not using ``run.sh`` directly
(an example of this can be found under the `Scaling and Load Balancing` documentation) or using the ``--no-create-venv``
option, explained in the `Options` section. It is also possible to force Galaxy to start without a virtualenv at all,

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nsoranzo Jan 25, 2018

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Underscore missing after `Options` ?

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@natefoo

natefoo Jan 26, 2018

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I guess I was thinking of Sphinx syntax for cross refs which don't carry the following underscore?:

:ref:`cross ref`

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automatic fetching of pinned dependencies.
`Conda`_ and `virtualenv`_ are incompatible. However, Conda provides its own environment separation functionality in the
form of `Conda environments`_. Starting Galaxy with Conda Python will cause ``--skip-venv`` to be implicitly set, and
the currently active Conda environment will be used to install Galaxy framework dependencies instaead.

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@nsoranzo

nsoranzo Jan 25, 2018

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s/instaead/instead/

Be sure to create and activate a Conda environment for Galaxy prior to installing packages and/or starting Galaxy or
else they will be installed in the Conda root environment.
Begin by setting

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@nsoranzo

nsoranzo Jan 25, 2018

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Remove?

The simplest scenario to using uWSGI with the wheel-based dependencies is to
install uWSGI into Galaxy virtualenv (by default, ``.venv``) using pip, e.g.:
``run.sh`` should automatically set ``--virtualenv`` on uWSGI's command line. However, you can override this using the
``virutalenv`` option in the ``uwsgi`` section of ``galaxy.yml`` as described in the `Managing dependencies manually`_

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nsoranzo Jan 25, 2018

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s/virutalenv/virtualenv/

@martenson martenson changed the title from Update framework dependencies documentation to [18.01] Update framework dependencies documentation Feb 1, 2018

@martenson martenson merged commit a37b638 into galaxyproject:release_18.01 Feb 1, 2018

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@nsoranzo

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nsoranzo commented Feb 1, 2018

I think the small issue with the Options cross-ref is still unresolved.

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